Yes it does seem the first of four columns has 8 distinct numbers.
As a side note, is there any released HCP resting state data on a 164k mesh
or are they all 32k mesh?
Thank you,
David Hartman
On Mon, Jul 17, 2017 at 6:19 PM, Timothy Coalson <tsc...@mst.edu> wrote:
> You can get a text file containing the label names and keys for a map by
> using -cifti-label-export-table. It appears that this will have extraneous
> labels in it due to how the file was generated, but you can ignore the key
> values that aren't used.
>
> If you count the number of unique values in one column of the cifti file
> you opened, you will probably get the number you are expecting. It is
> simply that the values are not 1-7, but an arbitrary set of integers.
>
> The -cifti-parcellate command will automatically use the first map in the
> label file to compute within-label averages for its labels. It is probably
> not what you want to use to simply examine the label map. I'm not sure why
> it ended up with 8 rather than 7 parcels, though. As a side effect, you
> could use "wb_command -cifti-parcel-mapping-to-label" to generate a label
> file that should be much less cluttered, but we may have better advice on
> this soon...
>
> Tim
>
>
> On Mon, Jul 17, 2017 at 4:51 PM, David Hartman <dhartman1...@gmail.com>
> wrote:
>
>> Since calling in MATLAB: “ciftiopen('RSN-networks.32k_fs_LR.dlabel.nii',
>> 'workbench\bin_windows64\wb_command.exe')” gives me a matrix with 4
>> columns whose range is beyond the 17 or 7 corresponding to their functional
>> grouping, I have resorted to using wb-command hoping to get right
>> labelling.
>>
>>
>>
>> *Question:* Which wb-command should I use to read the labels and see for
>> the 32k mesh which networks the nodes belong to (ie. 1 to 7)?
>>
>>
>>
>> I tried using wb_command -cifti-parcellate rfMRI_REST1_LR_Atlas_MSMAll.dt
>> series.nii RSN-networks.32k_fs_LR.dlabel.nii COLUMN out.ptseries.nii,
>> but out.ptseries.nii returns a matrix 8×1200. But I am hoping for
>> something 32k×1 for the correct labelling, where each row is a number
>> between 1 and 7 or 17 corresponding to the group the node belongs to.
>>
>>
>>
>>
>>
>> Hope it is not too confusing.
>>
>>
>>
>> Thank you,
>>
>> David Hartman
>>
>> On Mon, Jul 17, 2017 at 3:09 PM, Harms, Michael <mha...@wustl.edu> wrote:
>>
>>>
>>> Hi,
>>> There are actually 4 different maps in that file. If you load it into
>>> Workbench, the name associated with each map tells you what each map is.
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>> -----------------------------------------------------------
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave. Tel: 314-747-6173 <(314)%20747-6173>
>>> St. Louis, MO 63110 Email: mha...@wustl.edu
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of David
>>> Hartman <dhartman1...@gmail.com>
>>> Date: Monday, July 17, 2017 at 12:21 PM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: Re: [HCP-Users] mapping HCP data into 7 functional networks
>>> (using Thomas Yeo parcellation)
>>>
>>> Hi,
>>>
>>>
>>>
>>> *Background:*
>>>
>>> Regarding the labels file, “RSN-networks.32k_fs_LR.dlabel.nii” which I
>>> thought should contain the 7 and 17 network parcellation, this file has a
>>> matrix of size 64984×4. What do the numbers in the 4 columns represent (ie.
>>> 1st column has a max of 44 and 4th column a max of 26). I was expecting
>>> a single column that took values from 1 to 17 or 1 to 7 mapping each vertex
>>> to its grouping in the functional networks.
>>>
>>>
>>>
>>>
>>>
>>> *Question:*
>>>
>>> How should I understand these 4 columns and their connection to
>>> functional network parcellation?
>>>
>>>
>>>
>>> Thank you,
>>>
>>> David Hartman
>>>
>>> On Fri, Jul 14, 2017 at 2:27 PM, David Hartman <dhartman1...@gmail.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>>
>>>>
>>>> *Background:*
>>>>
>>>> Regarding the parcellation of the cortex into functional networks (“The
>>>> organization of the human cerebral cortex estimated by intrinsic functional
>>>> connectivity,” Yeo et al.) Yeo breaks up the cortex into 7 networks.
>>>> However, his cortical data has 163842 vertices, while the HCP data only has
>>>> 59412 vertices.
>>>>
>>>>
>>>>
>>>> *Question:*
>>>>
>>>> I am looking to map the HCP data into these 7 networks, but I don’t see
>>>> a way to get the data into the same format as Yeo’s data (ie. 163842
>>>> vertices) to use his mapping.
>>>>
>>>> 1. Does anyone know of a way to convert HCP data into the same format
>>>> as Yeo’s data to use his mapping or a direct way to map the HCP data to 7
>>>> networks?
>>>>
>>>>
>>>>
>>>> Any help would be much appreciated.
>>>>
>>>>
>>>>
>>>> Thank you,
>>>>
>>>> David Hartman
>>>>
>>>>
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>>
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